Antioxidant activities of various yogurts were assessed using different sample preparation procedures. Specifically, full-fat cow, goat and ewe yogurts as well as cow yogurts with different fat content (4%, 2% and 0%) were employed. Antioxidant activities were determined in two different water-soluble yogurt extracts and also in a total yogurt preparation using the “Clarifying Reagent” for dairy products. Full-fat ewe yogurt preparations exhibited higher antioxidant activities in FRAP and Folin assays as well as higher scavenging capacities against DPPH, hydroxyl and superoxide anion radicals than full-fat cow and goat yogurt preparations. Bradford, Lowry and Ellman’s assays confirmed that the strong antioxidant potential of the ewe yogurt was associated with its high protein content. In addition, antioxidant activities appeared to be related with the fat content of cow yogurt. Particularly, in DPPH, FRAP and Folin assays, and also in assays for scavenging of DPPH, hydroxyl and superoxide anion radicals, it was demonstrated that the fat removal led to the increase of the antioxidant/scavenging activities of the cow yogurts due to the increase of their protein/peptide water-soluble content. Moreover, for the first time, results show that the “Clarifying Reagent” for dairy products can be used for the determination of antioxidant and radical scavenging activities of whole yogurt using the FRAP assay as well as the hydroxyl and superoxide anion radicals scavenging assays.